[gmx-users] parameters problem

[Justin Lemkul]

On 3/11/14, 6:32 AM, Nidhi Katyal wrote:
> Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well
> as [molecule] entry. I have followed the following procedure to #include
> while creating my first molecule:
> Run pdb2gmx command.
> Added #include "ligand.itp" after
> #include "charmm27.ff/forcefield.itp"
> but before
> [ moleculetype ]
> ; Name            nrexcl
> Protein_chain_A     3
> and added at the end:
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> LIG                 1
> SOL             17063
>
> then I have merged protein and ligand coordinates by inserting ATOM lines
> from ligand.pdb to *.pdb generated after pdb2gmx command.
> Then. I run editconf, genbox and finally grompp command.
>
> After which I got following error:
> Fatal error:
> No such moleculetype LIG
>
> My both *.itp and *.pdb files contains LIG.
>
> How to rectify the error? Thanks in advance.
>

Residue name and [moleculetype] name are not necessarily equivalent.  You'll 
have to post the actual content of lig.itp to get any real useful diagnostic 
feedback.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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